Settings
QC
Quality control was performed on each processing stage. The final QC metrics for the aligned BAM files are shown.
Summary: Good and relatively uniformly mapped data
Load data
[1] TRUE [1] A A A B B B C C C D D D
Levels: A B C DCorrelation matrix
Dendrogram
Principal Components Analysis
| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 20.22 | 12.59 | 5.992 | 4.875 | 4.499 |
| Proportion of Variance | 0.5575 | 0.2164 | 0.04897 | 0.03242 | 0.02761 |
| Cumulative Proportion | 0.5575 | 0.7739 | 0.8228 | 0.8552 | 0.8829 |
Helper functions
Comparison
Differentially espressed genes (DEGs) detected at False Discovery Rate (FDR) 0.1. See the total number in the table’ annotations. Top 50 or less DEGs are visualized.
Legend for gene lists: “Geneid”, “symbol”, “description” - gene annotations; “Length” - length of a gene in bp; “logFC” - log fold change; “logCPM” - average Counts Per Million, log2; “LR” - log-likelyhood; “P.Val”/“adj.P.Val” - non-/FDR-adjusted p-value.
DEGs_1: Compare the scramble control without erythroid differentiation to the knockout without erythroid differentiation
DEGs_2: Compare the scramble control with erythroid differentiation with the knockout with with erythroid differentiation
Functional enrichment analysis
Up- and downregulated genes are tested for enrichment separately. Only genes at FDR < 0.1 are analyzed.
Each table has enrichment results for up/downregulated genes. The “direction” column indicate which pathways are enriched in “UP”- or “DN”-regulated genes.
Use the “Search” box for each table, to filter the results for “UP” or “DN” only. Search is global within the table, case insensitive.
FDR cutoff of the significant enrichments - 0.3.
Legend: “database” - source of functional annotations, “category” - name of functional annotation, “pval” - unadjusted enrichment p-value, “qval” - FDR-adjusted p-value, “genes” - comma-separated differentially expressed genes enriched in a corresponding functional category, “direction” - UP/DN, an indicator whether genes are up- or downregulated.